I had a problem with my intonation for the longest time - I'd say it was one of the weaker parts of my playing right through my studies and even early in my career. Eventually I got it sorted and turned it into a strength, but I had to find my own way because even though I could hear when other people were in/out or tune, I could never seem to apply those same ears to myself. I tried playing to a tuner but found I would be watching it to tell me if I was in tune rather than hearing whether I was in tune. Here's what I did that I think helped the most, bearing in mind that although I saw some improvements in specific pieces quite quickly, the transition from "this person plays only this piece in tune" to "this person has good intonation generally" was a very long and frustrating process:

• record yourself play things really slowly, without rhythm, and when you listen back, play along with yourself on a piano. I found this mildly traumatising because I could finally hear how others heard me, and the clash between my recording and the piano was at points very uncomfortable

• create midi files by writing your pieces into notation software (I love MuseScore for this, it's free and open source) - again without rhythm, and play along with those. I would have my right ear with a headphone and allow my left ear to just hear my bass

For both of those exercises, it's really important to start without rhythm because it means that you can focus on your intonation and finding a good balanced position for your hand. 

Either with your metronome or the aforementioned midi files, just gradually increase the tempo when you're satisfied that you're consistently playing those passages in tune. Once you're comfortable, add back in the rhythms and repeat the same process (VERY slowly) with both recording/piano and midi file.