what is the best Home theatre system under 1000 dollars?

Onkyo is a respectable brand, which also has a high-end line – INTEGRA.
In the $1000 range, the HTiB systems are about the same soundwise – bright, sharp, no real bass. Acceptable for movies, not really usable for music – unless you use 192kb doanloads.
If this is your range – go by features, quality of built (avoid plastic enclosure for speakers), etc.

There is always further reading about Niche Blueprint 2.0 Review here.