they stop and frisk people on the street in NY too
You can say no, but then you shouldn't walk on the streets.
I smell sarcasm! :) But seriously, riding the subway is not a right. They make rules for the subway and enforce them at their own leisure. But it's 100% legal to turn someone away if they don't comply with rules they make up themselves. MTA is a private entity.
Legally speaking they need "reasonable cause" to stop and frisk people on the streets (how that works in practice is a whole different discussion). At the subway entrance they can search all the bags they want for any or no reason.