If you're going to have it clipped, it's far easier to have it done now rather then a few weeks from now. It's hard to watch, but the area is numbed and it's really not uncomfortable for the babes.
The thrush is probaby the biggest cause of the pain, but has it always been painful to nurse? Just when your son latches or for the entire feed, and afterwards? A tongue tie can definitely inhibit a decent latch and cause feeding difficulties as well as a painful latch.
If it were me, I'd get it clipped, but I'd probably also want a second or third opinion. I'd probably contact La Leche and see if you can go to a meeting. They are a wealth of information with so much support and encouragement and someone will be able to evaluate the latch, the tongue tie, the thrush, etc.
Also, good for you for sticking with it! Breastfeeding can be tiring and difficult at times, and it can be so demoralizing to constantly face struggles, especially when you are tired and learning the ropes of new motherhood. It does get easier, I promise. :)