If you've got a $1000 budget on a "it might get stolen" bike you could do very well with Craigslist.

You might find something that's scratched up and in need of a little TLC, with plenty of room in the budget for replacement parts to make it something that looks beat up but is very ridable. That's a good mix between something that you enjoy riding that looks like it wouldn't be enjoyable to ride to a would be thief.