I am inclined to guess Bonju, at 6, off the port railing, with Hoban at I22 and here is why (aplogies for the length beforehand):
There are some inconsistencies that can be explained and some that can't.
Linae claims to have seen Anshu go below deck at the beginning of the storm (she presumed for medical supplies) then helped Anshu repair a leak below deck toward the end of the storm.
The Captain very well could have told Anshu to go below deck at the beginning of the storm, but Linae did not know about the leak so assumed it was for medical supplies. Anshu admits to coming back above deck an hour into leak-fixing when he heard yelling, assuming someone was hurt. During this time he could easily have been seen on the deck by many other crew members, helped out, went back down to repair the leak which Linae helped him with toward the end of the storm.
When Anshu said he saw Hoban at 5:00 "arguing" with "someone" on the aftdeck, I believe he meant Bonju, hence he approached Bonju just after that inquiring as to what was bothering Hoban.
Anshu claims Bonju says he didn't know what was bothering Hoban.
Bonju, in his story, claims to know Hoban was bothered by Linae.
In fact, Bonju is the only one that won't admit (to his crew) he knew Hoban was bothered by Linae, when it was no secret at all to the rest of the crew already (including himself).
Hoban was seen at 5:00 and all hours prior to that time.
Orrin, through a porthole (only located on the port side of the ship -- except in one, hopefully an artist's flaw in Chapter 2), claimed to hear someone scream and see someone fall overboard.
Bonju claims to have been doing dishes when he heard the Captain call, but Kentari claims he witnessed Bonju coming out of the weapons room with a knife when he heard the Captain call.
Linea claims to have witnessed Hoban and Anshu arguing just before the Captain's call. Anshu's story confirms this, admitting the argument reached a crescendo when he heard the Captain call.
Bonju is nowhere to be found at the end of the storm when the Captain notices Hoban missing.
I think the red ink on the grid represents their overall expected and planned course to Mystery Island.
Assuming the Map with the islands and ships represents their original intended course to Mystery Island (remember they didn't make it there first, so were then headed to Krawk Island), overlaying the Grid and Map and considering the X on the other side of the arrow to represent their pre-storm location, one could conclude:
G19 represents where they were before the storm blew them off course. The red circle below that represents their location was after the storm blew them off course. The arrow represents the actual stormy course. Hoban must have fallen off somewhere inbetween the two, any by the sight of the boxes floating away from the ship, I am betting Hoban drifted away from the ship, too.
Assuming his last view Hoban sees of the ship is of the port side (nevermind that in his "assumed view" there are no port holes heh), he must be drifting away from the ship near I22.
EDIT: Yep, Chef Bonju lied two times, that just about did it for me. Dishonesty bugs the heck out of me. The rest of my decision is based on the "facts" as I interpreted above, plus my own nautical "skills".
Who pushed Hoban? Bonju
When did he fall? 6:00
Where on the ship did he fall? port railing
Where is Hoban now? I22
Do you like Hoban's hat? yes, it's very stylish
(Further edited for elaboration on details only, my opinion has not changed.)