I've travelled with Intrepid & can recommend them - had a great time. I've come across a couple of GAP groups while travelling in S America. It seems there's a lot of Americans in their groups, which to me would be a little off-putting, but others mightn't mind that...
For flights, your best bet is to search using sidestep.com - it trawls all the other search engines and I've always found it to be good value. If you're prepared to take a chance. you can set an alert to keep searching daily/weekly which can save you a fortune (or cost a packet!) if fares change.