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How many Instant clients do you have 'installed' on your machine now?
Generally speaking, you'll want to match the bit level to your OS, and use a version that is at least as high as the version of the database you'll be working with.
Make sure the version you want SQL Developer to use is the first one listed in your OS Path environment variable - or some people actually install the client directly to their SQL Developer/bin directory - not necessary, but a nice 'lazy' solution...until you upgrade of course.
I do suspect yours is not a problem of compatibility between SQLDeveloper and instant client, but with the ojdbc6.jar file shipped with SQLDeveloper and the instant client.
You should try to set an ORACLE_HOME variable pointing to your most recent instant client installation, this way SQLDeveloper should be able to pick up the correct ojdbc6.jar shipped with your instant client of choice.
You can check the currently selected ojdbc6.jar by lookin at the property
Help -> About -> PropertiesObviously the instant client you point to should be of the same "bit level" of the SQLDeveloper installation as Jeff already pointed out.