The highest amount of experience per mission come from the Kaidan repeatable story missions. Some of them are short enough to be repeated comfortably and also have side missions attached to them.
Contract Killers (Bathhouse)
Spiral (Yuichi’s Apartment)
Youth Outreach (Rabbit detective)
Assault on Orochi Tower (Tower tunnel)
I also like Venice Sinking (Venice) and My Bloody Valentine (Clubhouse) but these two can take significantly longer depending on your familiarity and gear.