3am is the witching hour stuff so I get why that timing freaks people out, but honestly before jumping to poltergeist activity you need to rule out the boring explanations first. Pipes knock like crazy when pressure changes overnight, and animals in the walls are more common than people realise.
That said - if you've already checked that stuff and its consistently at the same time every night, that's worth paying attention to. Patterns matter with this kind of thing.
Have you tried recording it? Even a cheap mobile propped up down there would give you something to work with. Audio evidence is way more useful than people think, especially if you can rule out environmental causes by cross-referencing temperature logs or whatever. I've done this with a location in WV that had similar activity and the recordings picked up stuff you couldn't hear in real time.
What's the house history? Age, previous owners, anything unusual happen before you moved in? That context changes everything.