Can you please clarify your query?....are you looking for a custom/designer restriction enzyme for a specific sequence......or you are looking for designing a restriction site in your sequence...
Try to use a trial version of VNTI Software (http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/vector-nti-software.html) with updated enzymes database. Anyway, when you tried NEBcutter, did you try all commercially available specificities?
You can do an in vitro SELEX with a random primer base for your restriction recognition sequence. But this is a massive task that will take at least several weeks and needs a very good readout/selection criteria system designed.
It is more likely if you just want some short test if some polymorphism is there to look into the surveyor assay from NEB.