I don't remember much about the stated benefits of bee pollen, but Manuka honey has some unique antimicrobial properties due to the bees feeding on the Tea Tree and related plants. It can be used topically for wound healing for that reason, and some say those properties survive the digestive process to be active in the stomach and intestinal tract as well. There is some evidence that is has anti-inflammatory action and can stimulate the immune system. So that's one major difference between the two. I suppose it depends on what benefits you're looking for.
I think Manuka honey may have helped me kick a lingering upset GI system thing I had going on. I ate a teaspoon in the morning and added it to my tea. You do, however, want to be sure you purchase a brand that has either a number rating of UMF or MGO. (They measure the amount of active chemical components in the honey. It's less clear that the "Active" rating system is as reliable, so beware.) The MGO and UMF brands are more expensive, though! I bought the most reasonable one I could find, a small MGO 400 strength jar from Amazon, and it wasn't too bad at around $25.
From what I remember, bee pollen is more of a general "superfood" thing touted for general well being and energy levels.