I'd always first look at power. The Sidewinder has a good enough generator, so look at the power distributor first. You should be able to get a C1 or C2 (always forget which) that gives you all blue numbers in the comparison and comes at a really good price, so you can boost more frequently, and your shields and weapons are both markedly improved.
After that, it's a matter of taste. You can upgrade many systems with a minimal impact on weight, so you can look at your needs; you can upgrade thrusters for better maneuvering in normal space, or the FSD to increase jump range, upgrade the shield generator for obvious reasons, and so on. Just make sure your "deployed" power draw is covered by the generator and your jump range doesn't get too short.
The Eagle can be upgraded quite decently (I was running almost all C rating, the two loaner lasers on the bottom and a gimbaled multicannon on top) which produces quite the durable little beast for under 100k credits. If you want to do combat, that'd be the option I'd recommend.