You're totally right I would definitely always say "my favorite team is", and probably also would say "my favorite is". I think the subject of the sentence is what determines it grammatically, also since that's what you say first it makes sense it would affect your choice of verb more.

I actually think this could extend to a lot of situations where the object is referring to a single group, not just plural-sounding proper nouns. Like if asked "what was your favorite zoo exhibit?", I would probably respond "my favorite was the giraffes" not "my favorite were the giraffes". I'm actually not even sure what the correct response would be technically though. "My favorites were the giraffes" implies multiple favorites, and "my favorite was the giraffe" makes it sound like the exhibit had a single giraffe. So it feels like subject/object have to mismatch then.