Is there a polynomial time algorithm to tell if an NFA over an unary alphabet is universal? Given an Nondeterministic Finite State Automaton with $n$ states over an unary alphabet, is there some algorithm to check if the automata is universal in time polynomial in the number of states?

I would not expect this would work over an alphabet of size two or more, since it is PSPACE-complete to check whether a regular expression is universal. However, since regular languages over unary alphabets have nice characterizations, I would expect there would be some way to check the universality of an NFA over an unary alphabet.
Determining whether a unary NFA is universal is coNP-complete, as proved by Stockmeyer and Meyer, Word Problems Requiring Exponential Time. See Gruber and Holzer, Computational Complexity of NFA Minimization for
Finite and Unary Languages, for more results in this vein.