I'd recommend exiting at Waterloo. We stayed there last year (Park Plaza County Hall, across the street from Park Plaza Westminster) and it was very convenient, especially with luggage. The train station is large and it's easy to get funneled out at a weird exit. If you can, follow the signs towards the Sidings mall area, and exit just before you get to Brewdog. Follow the exit, turn left on the sidewalk at the main road (York Road) going past the Premier Inn, and then you'll end up at both Park Plazas.
I'd vote for the Elizabeth Line to Northern, mostly because the Elizabeth Line is so nice! It was quiet, efficient, and cool. Because we were staying near Waterloo and due to our other destinations, we didn't ride it again, so it was nice to ride that first trip in.
Piccadilly Line was closed when we were there, so we switched at Bond St to Bakerloo because we also needed to stop at Picadilly Circus on the way for an errand. Bakerloo was not our favorite, it's louder and older, my husband did not like the squeaky brakes much. Definitely being picky though, it still got us where we were going!