How much can I expect to spend on a decent kayak?
Inflatable kayaks start at about $200, and a good sea kayak can cost you up to $3000.
I'm not really interested in an inflatable;  How good is a decent kayak for use on a lake?
A sturdy and quality kayak will probably cost you around $1000. If you don't mind the quality being a little less, than it can be cheaper than that!
What are the best brands at around $1000 and any I should definitely stay away from?
Ocean Kayak is a brand that has really great reviews. Old Town Kayaks also have a reputation for being very dependable. You might want to stay away from Advanced elements kayaks because they are inflatable.
Do the kayaks come with paddles at that price, or will I need to buy then paddles separate.?
It seems you will have to buy paddles separately. There are many different kinds depending on your skill level.
I'm pretty advanced, but my son will also be using the kayak. He's not as skilled.  Should I really buy him separate paddles?
Yes you should buy him separate paddles. They make paddles that are designed just for kids. They are smaller and well balanced.