When it is sounding, boogie and listen at as many heating and vent ducts and pipes (both water and hot water baseboard as possible (may take several instances to track down), if you have them) to see where noise is coming from. Likely sources for this type sound, which may actually be occurring all day but you only hear when it is quiet at night before or after you go to bed or when in a certain place in the house:
1) furnace fan
2) garage unit heater fan (direct-fired gas, electric, or hydronic heating system)
3) whole-house ventilation system fan or A/C compressor or heat pump
4) hydronic or steam radiator/baseboard heater/in-slab heater circulating pump
5) floor drain sump pump
6) sewage lift pump, if you have one - either in house to lift to sewer outside, or to lift sewage to an uphill septic tank/leach field
7) rarer, but sometimes heard if you have a lift or pump station near your house, sewage lift pump or water system booster pump or standpipe/water tank refill pump in the public mains - normally would not be heard unless within a block or less of your house - your water and sewer utilities could tell you (probably engineering department) if you have one nearby
8) heat-pump type water heater
9) if you have a french drain system with a collection well, it may have a sump pump that runs periodically
10) if on a well, well pump repressurizing system periodically even if you are not using water, if it is leaking off pressure due to a leak or a leaking footvalve.
11) humidity-switch controlled ventilation fan in attic, basement, crawlspace, under stairs, bathroom
12) noisy neighbor's A/C or heat pump if facing your house
From your motorboat engine dying description and since you say vibrating, my first guess would be an attic ventilation fan, A/C condensor (outdoor) fan, garage unit heater fan or hydronic heating system circulating pump possibly with bearings starting to get loud due to lack of lubrication or just plain old age wear and tear. The motorboat engine dying sound could also be water running back through the outflow pipe back into the sump (no backflow preventer or not working) after the pump stops pumping out - though 2-5 minutes would be a long time for a sump pump to run, but if you have a lot of water under your basement slab so it is basically a covered bathtub can happen.