I think the best option is to have a simple book bag, put the iPad in a case then in the bag. Small iPad-sized bags will tend to be a dead give-away. I keep mine in a bookbag when on the subway. I only take it out if I have a seat near the center of the car (not near the doors) -- I'm more likely to take it out if other people have devices out too.
My bag has snaps on it and I loop one through my case so if someone snatched it they would pull me and my bag along too!
I decided, also that I could not live in fear forever. Not being able to use my fun iPad on the train because I'm scared sucks. It makes the device less useful. But, if you never risk you never live. I'm not rich, but really, even if it were stolen, I can save up for a week or two and buy a new one, it's just a *thing* I won't ever forget that. LIVE. Don't let the scum of the earth cramp your ability to enjoy life!
I once saw a man try to grab an iPod touch from a young kid. The kid cried out and lunged, the thief was grabbed and tripped by multiple train passengers. The iPod fell on the ground** and the thief got away. The iPod still worked and we all comforted the kid and cheered for him since his iPod was fine. NYC is a tough town.
Alternately ,you could find a removable sticker that said "GALAXY TAB" and stick that on the back....
** This is why I bought drop insurance. I have a feeling that an attempted robbery would result in my iPad being dropped... and I'm clumsy.