Cows
There is one specific mention of owning cows, which is the fictional innkeeper in the song Frodo sings at Bree, which is a song that it's implied Bilbo would frequently sing in the Shire, implying perhaps that it applies equally well to Hobbit owned inns.
Then in desperation he began a ridiculous song that Bilbo had been rather fond of (and indeed rather proud of, for he had made up the words himself)...
They also keep a hornéd cow as proud as any queen;
But music turns her head like ale,
And makes her wave her tufted tail and dance upon the green.
The Lord of the Rings - Book I Chapter 9 - "At the Sign of the Prancing Pony"
There are also mentions of products that can be derived from cows, such as butter, cheese, milk, bones, fat and cream. These can also be derived from other animals though, and so they are given their own category below.
Pigs
There are some references to food products that would specifically only apply to pigs. In one of these cases, the bacon is listed as an example of Hobbit "farmhouse fare", implying that it was raised there, not just imported from out of the Shire.
There was beer in plenty, and a mighty dish of mushrooms and bacon, besides much other solid farmhouse fare. The dogs lay by the fire and gnawed rinds and cracked bones.
The Lord of the Rings - Book I Chapter 4 - "A Shortcut to Mushrooms"
“And pork-pie and salad,” said Bombur.
The Hobbit - Chapter 1 - "An Unexpected Party"
He did not go much further, but sat down on the cold floor and gave himself up to complete miserableness, for a long while. He thought of himself frying bacon and eggs in his own kitchen at home—for he could feel inside that it was high time for some meal or other; but that only made him miserabler.
The Hobbit - Chapter 5 - "Riddles in the Dark"
Chickens (and perhaps other egg-laying fowl)
There is one specific reference to (cold) chicken, and one reference to domesticated fowls being kept in yards, but there are also many references to Hobbits eating eggs (such as the "bacon and eggs" references given elsewhere).
“Put on a few eggs, there’s a good fellow!” Gandalf called after him, as the hobbit stumped off to the pantries. “And just bring out the cold chicken and pickles!”
The Hobbit - Chapter 1 - "An Unexpected Party"
Soon after six o’clock the five hobbits were ready to start. Fatty Bolger was still yawning. They stole quietly out of the house. Merry went in front leading a laden pony, and took his way along a path that went through a spinney behind the house, and then cut across several fields. The leaves of trees were glistening, and every twig was dripping; the grass was grey with cold dew. Everything was still, and far-away noises seemed near and clear: fowls chattering in a yard, someone closing a door of a distant house.
The Lord of the Rings - Book I Chapter 6 - "The Old Forest"
Bilbo and Gollum are also both familiar enough with eggs to have it as an answer to a riddle.
A box without hinges, key, or lid,
Yet golden treasure inside is hid,
he [Bilbo] asked to gain time, until he could think of a really hard one. This he thought a dreadfully easy chestnut, though he had not asked it in the usual words.
... But suddenly Gollum remembered thieving from nests long ago, and sitting under the river bank teaching his grandmother, teaching his grandmother to suck—“Eggses!” he hissed. “Eggses it is!”
The Hobbit - Chapter 5 - "Riddles in the Dark"
Other evidence of livestock
As discussed above there are multiple references to animal products, such as butter, cheese, milk, bones, fat and cream. Many of these can be derived from several different types of animals, including cows, but also from animals that are not listed above, such goats and sheep.
A big jug of coffee had just been set in the hearth, the seed-cakes were gone, and the dwarves were starting on a round of buttered scones, when there came—a loud knock. ...
“What’s that? Tea! No thank you! A little red wine, I think for me.”
“And for me,” said Thorin.
“And raspberry jam and apple-tart,” said Bifur.
“And mince-pies and cheese,” said Bofur. ...
Cut the cloth and tread on the fat!
Pour the milk on the pantry floor!
Leave the bones on the bedroom mat!
Splash the wine on every door!
The Hobbit - Chapter 1 - "An Unexpected Party"
So he sat himself down with his back to a tree, and not for the last time fell to thinking of his far-distant hobbit-hole with its beautiful pantries. He was deep in thoughts of bacon and eggs and toast and butter when he felt something touch him.
The Hobbit - Chapter 8 - "Flies and Spiders"
The fruit was so plentiful that young hobbits very nearly bathed in strawberries and cream; and later they sat on the lawns under the plum-trees and ate, until they had made piles of stones like small pyramids or the heaped skulls of a conqueror, and then they moved on.
The Lord of the Rings - Book VI Chapter 9 - "The Grey Havens"
Non-livestock animals (dogs, cats, and ponies)
While probably not considered livestock, we have a very specific example of a Hobbit owning dogs, which is more direct than can be said about just owning food products (which could perhaps have been traded for).
‘What’s wrong with old Maggot?’ asked Pippin. ‘He’s a good friend to all the Brandybucks. Of course he’s a terror to trespassers, and keeps ferocious dogs – but after all, folk down here are near the border and have to be more on their guard.’
The Lord of the Rings - Book I Chapter 4 - "A Short Cut to Mushrooms"
The inn in Bilbo and Frodo's song has a cat a dog.
The ostler has a tipsy cat that plays a five-stringed fiddle;
And up and down he runs his bow,
Now squeaking high, now purring low, now sawing in the middle.
The landlord keeps a little dog that is mighty fond of jokes;
When there’s good cheer among the guests,
He cocks an ear at all the jests and laughs until he chokes.
The Lord of the Rings - Book I Chapter 9 - "At the Sign of the Prancing Pony"
And there are references to Hobbits owning ponies.
When they had finished, the farmer and his sons went out with a lantern and got the waggon ready. It was dark in the yard, when the guests came out. They threw their packs on board and climbed in. The farmer sat in the driving-seat, and whipped up his two stout ponies. His wife stood in the light of the open door.
The Lord of the Rings - Book I Chapter 4 - "A Short Cut to Mushrooms"
‘The answer to the second question,’ said Merry, ‘is that we could get off in an hour. I have prepared practically everything. There are five ponies in a stable across the fields; stores and tackle are all packed, except for a few extra clothes, and the perishable food.’
The Lord of the Rings - Book I Chapter 5 - "A Conspiracy Unmasked"