If you absolutely must have air conditioning in hot weather or heat in cold, the two cars of the that are always reliably temperature controlled are the first car, where the motorman sits, and the middle car, where the conductor (the person who makes announcements and opens and shuts the doors) is. Neither of those two unionized parties will work in environments without reasonable temperature control — the train would simply be sent for maintenance otherwise — and you can take advantage of that fact for your own comfort.
Of these two cars, the first is more likely to have seats or liberal standing room than the other.
If you find yourself in a train that is entirely without human operators, I suggest you write an angry letter to the Mayor.