I'm currently using 3-position JST connectors with two of the wires cut off, but this is unsatisfying. The 3 position JST is also bulkier than I'd like, and has lots of "barbs" and corners to catch on things, which is undesirable for my application (wearable electronics.)
The connector will be carrying signal at 5V, so the current requirements are low.
I would go for single pole "bullet" connectors. Common among RC hobbyists as a connector between battery pack and system. To make them more streamlined you could apply some heatshrink tube.