Given the increasing prevalence of limited runs (and of shorter runs for most things that open even without an announced limit), it's inevitable that with one trip a year you're going to miss a lot of things you might want to see. I typically do two big trips a year, one in early November and one in late April/early May, and I've found those times generally work well (though even then there are many things that fall in between that I'm sorry to miss - like Eureka Day). If I was only going in April/May, I would never have seen some of the highlights of my trip last month, including Ragtime, Yellow Face, Swept Away, Hills of California, and (possibly) Maybe Happy Ending.
But if you can only swing one trip a year, I'd go with late April/early May. The weather is better, the hotels are generally cheaper than in November, and many of the prime Tony candidates will have just opened. Another perk is that because you're in the middle of nominations and voting, there's usually less of a chance that any particular performer who you really want to see will be out.