I was in the same exact position a few months ago. I had been going to Toyota and was being charged an arm and a leg, and in addition, I strongly suspect they were cutting corners with the work they were supposed to be doing.
I searched our sister board, Astorians.com and decided to go with one recommendation, Paul's Getty at 43-10 31st Ave, 718-274-2688.
I've only been there once and don't know cars well, so it's hard for me to give a strong recommendation, but I will say that I felt good about the experience and comfortable that I was being well taken care of and not tricked into having things done that don't need to be done. Paul explained everything and broke it down into 3 portions: 1 was work that absolutely needed to be done right away, and the other 2 categories were a bit more optional or could wait. He didn't pressure me in any way. He knew that my bf knows cars well (but lives in another state) so he suggested I call him and talk it over before making a decision about what work to go forward with.
He seemed pretty shocked when I told him that only 7,000 miles earlier I had had the complete 60,000 mile workup done at the Toyota dealership but he also didn't want to badmouth other mechanics and since it was a done deal with toyota, we didn't really go into what they had done incorrectly or badly.
I ended up doing all three categories of suggested work and the car runs very smoothly now and when I need to, I will go back to him again.
also, when the car was ready, he had one of his guys drive my car over to JH to pick me up and then I drove it back to the shop to pay. (It's also close to the subway if you don't want to do this.)
I wanted to add that Paul's been in business for years and is from that neighborhood and probably can't afford to cheat his customers as they would stop coming and stop referring people. Toyota can get away with this (if that is what is going on there) because people will continue going to the dealership without being referred.