Yes, they were meant to be as parts of a greater whole. The Season 5 standalone adventures("Modules") happen at the same time as the Storm King's Thunder HC book, and can reference the same plotline/events/characters from the book. You can even interlace some of the S5 mods in between the chapters of the book, and should be able to maintain the same adventure feel.
Edit: I myself run just the modules as I get more drop-in/drop-out players at the stores where I DM. The HC adventures work better with a more consistent group of players. You can use one, the other, or both!