There is already a fair bit of info on this out there but this is the way I check carts to see if they're legit or boot.
You can look at the shell and label by all means, but a boot cartridge case or repro label doesn't mean the boards inside aren't legit. Bootleg cases tend to have a slightly different shape or texture than real ones, sometimes they're the wrong colour too. If you go back a month or so on here you'll see where I picked up a bundle of 5 carts, one of which was in a boot case. That's blue but a different shade to the legit blue cases. It's also a little chunkier than a real cart. The boards inside that are real. I've since aquired a legit cart case to pop them in. The only boot cart I still own has a black case but it has a matte texture, not smooth and glossy like real carts.
Anyway, boards can be moved between cases, labels can be mutilated or removed or replaced. That doesn't mean the boards aren't legit.
The only real way to tell is to look at the PCBs. What you want to do is compare them to the ones you find here:
it's an awesome resource showing legit PCBs and labels and also some boots. The problem is that opening up the case to look properly at the boards can damage the label. Not something you want to do if it can be avoided. So here's what I do.
First I find out the unique identification code for each neo geo game; it's NGH number. On a legit board the ROMs (generally toshiba) will have that code printed on them.
Check here for the NGH number http://www.neogeosoft.com/?section=mvs
If the chips are in the right place (check the scans page). Are proper mask ROMs not EPROMS, and have the right number on then the cart is almost certainly legit. Luckily you can get that info without opening the cart.
You want to turn the cart so that it has the insertion arrow down and the edge connectors towards you
Then peek through the bottom set of vents. Chip placements change a little by cart but normally you'll be able to see two ROMs and look for the NGH number.
If you look through the vents there you can see 224-P1. 224 is the ID for twinkle star sprites. Good. Legit cart. And no damage done to the minty label that's on there!