Clinton and Gingrich's relationship was worse than Obama and Boehner. The reason Gingrich was more "productive" is because the GOP controlled the Senate as well, so bills actually made it to the President's desk and he happened to sign a few. No compromise was really ever reached in the 90s.
After the initial government shutdown standoff, Clinton and the GOP Congress were able to reach subsequent budget deals much more easily than I imagine Obama will ever be able to with this Congress. But that's because the economy was booming and the government was flush with cash. The economy was strong enough that the president and Congress didn't really need to do anything new at that point in order to balance the budget. That's unlikely to occur again any time soon.