Sand or gravel?

I'm not sure what puffers would prefer, if any, but Sand is a great medium!

As for Vacs, if you do this 2x a week you can get away with "hovering" the vac just over the sunstrate, but every 4-5 weeks I would gently press the Vac about 3/4 to a inch down and gently raise to allow the sand particles to rest out. You will pick up some sand, but it very little in the scope of things.

Also, a periodic "stir" is a good suggestion for sand as well to open an aerobic pockets. I do mine every 4 months or so, but others may suggest different (I'm new to sand myself for the past year)

Be careful with how many puffers you put in there. I've read that you shouldn't put more than one per five gallons of water, and only with lots of places to hide at that. They tend to be aggressive and territorial. As a matter of fact, that goes for putting other fish in with them as well. I've never kept them, but I've heard many stories.

They are very territorial. I had 2 in a 10g and they were constantly chasing each other around, away from food, etc. As long as you have at least 3-4 good hiding spots you shouldn't see too much fighting, but you will see some.

Good video demonstrating sand cleaning technique: LINK

ct-death was right, you do need to either stir the sand periodically to prevent anaerobic pockets or have Malaysian Trumpet Snails which will do that for you. However, they wouldn't last very long in that tank as the puffers would take them out faster than you could imagine.

MTS breed fairly quickly, and some large chain stores hand them out for free.

three should be fine, and aggression will be spread out better. granted, this is also only if you have adequate hiding places.