The avenues in Manhattan actually flow really well and the lights are very well timed. You can get from downtown to uptown almost without stopping. Personally I don't think cyclists should be mixed with cars in Manhattan especially when there's already dedicated bike lanes. But I'll probably change my opinion once I start commuting via bike :)
The problem is that many of those bike lanes present significant problems to cyclists using them (illegally parked vehicles, lack of room to avoid bad surface conditions, intersection conflicts, dooring hazards caused by door zone bike lanes, etc.