My minecraft runs on about 60 fps, but when I am near the reactor (about 50-80 blocks near) my fps drops to less than 15.
My reactor is underground and I do not have direct line of sight to it, but I am still lagging.
I found that when I break one block of the reactor, the lag disappears. When I add the block and reactor reassembles, I am lagging again.

Edit:
I just found more details.
I have 2 access ports.
When the reactor is set to auto-eject waste and the access ports are already full with waste, it lags.
When I remove the waste to free space, the lag is gone.
So the cause of the lag is the process of searching where to eject waste.

Interesting. Which BR version are you using?

Lastest of course. 0.3.3A.

This should be resolved in 0.3.4A, there were several bugs in the waste distribution code.