Yale is pretty progressive and I saw it listed as one of the top 20 Trans friendly universities in the US (but those top 20 lists are unreliable). The rest of New Haven is either geared toward Yale or part of the neglected African American and immigrant Latino communities and they have their own socially conservative orientations regarding gender...Connecticut as a state has many protections in place and I would consider it generally Trans friendly...but there are pockets of social conservatives in the state too (for example, many Catholics...some of which are less tolerant).
Palo Alto. Never been. But it is in California, the state that, along with Massachusetts, are the most progressive in the country. Look at the websites of the LGBT centers on campus. Frankly though, if given the choice, an Ivy has a lot of weight though. So if it is Yale v. Palo Alto I'd choose Yale. If it is Yale vs. Stanford, that is a slightly more difficult choice. I cannot speak for Stanford but Yale has a real University vibe, tightly knit community(ies), etc. Plus it has seasons, snow, and is an hour and a half to NYC by train and 2 and 1/2 to Boston.
I moved to CT from the Midwest and I like it. Mind you, outside the university systems, for older Trans folk, Connecticut is, I feel, really lacking...but that is another story.
