IMO it's probably best to do H/C/I all at once and get parts that are matched to work together to meet your goals. This will save you from having to tear apart the engine multiple times (hopefully).
But if you have to space it out definitely get the intake first, but make your decision on which intake based on what heads you plan on getting down the line. You don't want to buy an intake now and then just have to sell it when you get your heads.