The best 3rd party controllers I've had are the Logitech F310 for PC (any PC controller is technically 3rd party, right?) and some MadCatz thing for the N64... I can't remember the model number but they were almost identical to the stock 1st party controllers with two distinct differences: they were thicker and they had better joysticks.

For the latter, I loved them because of the stick not the thickness. Back in those days, my siblings and friends all played a lot of WWF and Mario Party and those games took a heavy toll on the springs in the N64 controller. Eventually after a few sessions, the first party sticks were loose as fuck and barely functioned. Those MadCatz pads, however, were sturdy as fuck. You could full-palm the stick all day, every day and it would still snap back to center perfectly.