differential trace impedance for USB (90 Ohms) on 2-layer FR4 board
The reason the values differ so much is because different tools use different formulas to calculate impedance. Some are approximated closer than others, but finding exact impedance is extremely difficult if not impossible. The best tool I've used, and I still use today, is the EEWeb calculator (which you linked to in your post). That one seemed to have the best, most accurate results in my experience. There are also plenty of clones that use the same math as the EEWeb calculator so they will also be just as accurate.

Generally, when designing with controlled impedance as long as you get within +/-20% you will not notice much in the way of reflections and distortion, though of course this depends on frequency and switching speed. However, I try to shoot for about 10% over the target impedance. It's better for the Zd to be higher than the target than for it to be lower. 10% is pretty standard for most designs. In your case I'd shoot for a Zd around 100 ohms (basically 10% higher than your initial target).