Kudos for not wanting to work for a big corp, though sometimes they choice isn't yours. Your current startup might get acquired by IBM then you become an IBMer:)

I would like to think incubators care more about what you are doing than your platform of choice. At worse they may recommend you switch to some other platform, but no, I don't think any incubator worth being a part of would look down on you just because of your choice of platform.

If Java is the best platform for a product then by all means that's the choice you should make. For instance if you want to build a product that may need to be integrated with other products then that would need to be factored into your platform of choice.