Had something similar a few years back in my old house in Carlisle. Knocking sounds every single night, pretty much the same time. First thing I'd say is don't rule out the mundane stuff - pipes contracting in the cold, rodents, that kind of thing. Worth getting those checked first just so you can rule them out properly.
That said, the consistent 3am timing is interesting. A lot of people on here will tell you about the "witching hour" theory and honestly after doing spirit box sessions for a while now I've started to take that a bit more seriously than I used to.
What I'd suggest is try to record it. Even just your mobile propped up against the wall. Note down the exact times, how many knocks, any pattern to them. The more data you collect the better picture you build up. Has anything else unusual happened in the house alongside the knocking, or is it just that one thing so far?