I'm going to preface this with the same response as I did with the EML seats with children and carseats. It's going to ultimately come down to what the gate or ticket agent does. I have seen guitars and other large sided instruments come on board. I have also seen them make it to the gate and get gate checked. Personally, I will try to work with the customer so they don't have to gate check it. If I have seats I will try to move the customer and instrument to a seat where the instrument can be buckled into the window seat.
Here is the Official Policy from JetBlue:
Musical instruments can be checked or carried on, subject to space.
Musical instruments are subject to the same size regulations as any other checked or carry-on item. If the musical instrument is large and you'd like to carry it on, you may need to purchase a seat for the instrument, provided there is availability. The instrument or equipment must be secured in a window seat and cannot be secured in the first row or emergency exit rows.
Musical instruments are conditionally-accepted articles, and JetBlue cannot be responsible for damages.