Hello I just started playing guitar and I wanted to start off with a decent amp.

My Guitar: Schecter Damien solo elite 6

My budget: I would rather not go over $500

Bands I play: Muse, NIN, Bush, Creed, A Day to Remember, Chevelle, Atreyu

Id like to buy New so I'm not looking for something discontinued or hard to find.

A clean channel is very important to me as that's how I practice. Effects are not as important as I plan on buying pedals in the near future anyway.

I will be playing 80% in my room and 20% with a drummer and bassist.

I was looking at the Peavey VIPYR VIP 3, the Peavey Bandit 112, and the Crate FlexWave FW65 although I haven't actually played any of them.

Any ideas would be appreciated.
For the budget you're looking at, you can definitely do better than what you've listed, especially the Crate. What I would recommend is finding a decent used tube combo, probably a Randall or a Marshall would work best for you. If nothing else, get yourself a Peavey Valveking 2x12 combo. Much better tone than the Vypyr, and the clean channel has very nice definition.
Why don't you want to buy used?

Just think of the rig you could build with that much cash, with such a down market as we're seeing today.