Take a look at the Theoxenia Hotel on Santorini. It is in the middle of town in a great location. It is a small hotel and the guy that owns/runs it is great and will take excellent care of you.

On Mykonos we stayed at the Hotel Leto, which is also quite nice and is almost in town (maybe a 5 minute walk).

I think that both of those will fit into your budget nicely and are both good quality hotels that I would stay at again.