Maybe check the switch on the back of the TF to make sure it's set to amp level for the output, rather than line level.
If that's not the problem, then I'm wondering if you mean the whole level–including the dry–is lower out of the Crate than the Fender? If it's just the wet that's lower, then I'm guessing it's because the tube amp is compressing more than the crate? I use my TF through a Fender Hot Rod Deluxe set to sound clean and through a Marshall Plexi clone set to light overdrive. The delays compress (upwards) a lot more in the overdriven amp, so they sound louder.
