From my perspective they compliment each other... Judo takes off where Aikido left off.
In our higher kyu ranks we do koshinage, Sumi Otoshi, & Kubinage... moves which are a closer transition to what you would expect in Judo. [one, if not all of those are done in Judo]
Its really about range... Aikido is medium range for knives, etc.
Judo is close range for flipping/throwing and setting you up for ground fighting. [BJJ]
Somewhere in-between Aikido and Judo is the clinch and knees/elbows along with kicks & strikes further out, etc.
So from my perspective Aikido is a part of the larger whole.
Judo, Aikido, BJJ are a natural triangle... they all came from Jiu-Jitus and it shows... its like 3 brothers just walked off one day and forgot about the other and the strengths they offered.
Enjoy your training! [Judo is a bit rough for my body at the time, at least conceptually, though I wouldnt mind trying it out.]