I’m with the camp that says avoid NYC metro.
You could try something like this to be really effcient:
-Redeye into Boston leaving Wednesday night. Arrive Boston Thursday morning. Go to Amtrak station and locker luggage so you don’t have to take it everywhere.
-Visit Harvard and MIT
-Take Amtrak to Providence and check into a hotel.
-Visit Brown Friday morning.
-Take Amtrak to New Haven.
-Visit Yale. Take Amtrak back to Boston and fly back to CA on late flight.
I’d never do a schedule like that but it might be possible.