For the synergy feats in general it helps to go straight towards them, so 3 levels in one class 3 in the other and then one each so you can get them at levels 7, 8 and 12 respectively.
For nightstalker specifically I'd start with Rogue (you lose too many skill and tool proficiencies otherwise), then go through rogue and adept as it fits you till both are at 3rd level.
After that rogue or adept to 4 and then the other one to 4 and you got the first two synergy feats.
By then it's your decision if you want to be a "magic" ninja instead of a normal one, if so, decide which of your two legs (rogue/adept) you want to lean on more and get that to level 8 for the final synergy feat.
Checking on which class features you'll be "missing out" might help with the decision.