If you are content with the sound of your Bose/JBL combo, then I would advise you to stick with separates and buy a newer receiver and sub. HTIB is fine for smaller rooms and nicer decor, but it doesn't have the impact nor does it offer the upgradeability options of separates.

I like Yamaha and Denon for good-value receivers (lots of folks seem to like Onkyo as well). Athena, Paradigm, PSB all make good mid-range subs in the 10"-12" range. I think you'll be happier in the long run if you go separates.