The Schengen Borders Code restrictions on third-country nationals do not apply to your wife if you are an EU citizen or a citizen of an EEA country or Switzerland. See article 2, items (5) and (6), of the Schengen Borders Code:

5. ‘persons enjoying the right of free movement under Union law’ means:

(a) Union citizens within the meaning of Article 20(1) TFEU, and third-country nationals who are members of the family of a Union citizen exercising his or her right to free movement to whom Directive 2004/38/EC of the European Parliament and of the Council ( 1 ) applies;

(b) third-country nationals and their family members, whatever their nationality, who, under agreements between the Union and its Member States, on the one hand, and those third countries, on the other hand, enjoy rights of free movement equivalent to those of Union citizens;

6. ‘third-country national’ means any person who is not a Union citizen within the meaning of Article 20(1) TFEU and who is not covered by point 5 of this Article;

(5(a) covers EU citizens and their family members; 5(b) covers EEA and Swiss citizens and their family members, where in both cases "family members" is limited to the definition set forth in directive 2004/38/EC, which includes spouses.)

If you are not an EU, EEA, or Swiss citizen, the Schengen Borders Code does apply, and it requires her passport to be valid for three months (not six) beyond her departure from the Schengen area (not counting Portugal). See article 6. But this article is written with visitors in mind. In practice, the right of transit set forth in 6(5)(a) means that border inspectors are unlikely to pay close attention to the passport expiration given that she lives in the Schengen area:

5. By way of derogation from paragraph 1:

(a) third-country nationals who do not fulfil all the conditions laid down in paragraph 1 but who hold a residence permit or a long-stay visa shall be authorised to enter the territory of the other Member States for transit purposes so that they may reach the territory of the Member State which issued the residence permit or the long-stay visa, unless their names are on the national list of alerts of the Member State whose external borders they are seeking to cross and the alert is accompanied by instructions to refuse entry or transit;

However, I had a look at Norwegian's site and the visa-information company it refers travelers to, and both have a good deal of outdated or simply incorrect information. For example, someone in your wife's situation but holding a passport that normally requires a visa is told that they need a visa to visit Greece even if they say they reside in Portugal, without being asked whether they have a residence permit and without recognizing that someone residing in Portugal ought to have a visa already (or a residence permit, which substitutes for a visa). It then tries to sell you a $250 consultation. And nowhere does it mention nor ask about passport expiration. So you may find it difficult to get a straight answer.

If you're an EU/EEA/Swiss citizen, I suppose it's less likely that Norwegian would refuse boarding, but it's still possible that they don't know the law. If you can, find out what office in Norwegian is responsible for the policy that guides the worker who actually makes the decision when you arrive for the cruise, and get a written statement of their policy with respect to travelers in your wife's situation. This may be difficult to do; for example companies often shy away from making such commitments out of an abundance of caution, because facts could change, or something else unrelated might arise to cause them to change their minds. If you can't get any peace of mind from Norwegian, you might consider replacing her passport early.