It's honestly personal preference. Sure Jonin Minato will become better with his bond mystery, but Hokage Minato is still better at Decisive Bonds, Ranked Teams, and GNW cause of his mystery and his 40% resistance passive (looking at you AGK and Edo Hiruzen). Plus, getting Jonin Minato's bond mystery requires Boy Obito and Kid Kakashi (Kakashi can only be received through server merges, there are plans to make him available through events) and the Bond mystery is pretty much P2W at this point. So saying Jonin Minato currently is better than Hokage Minato is misleading.

Now, getting Hokage Minato vs Madara [5 Kage] or newer ninjas? Well, we still have no definite word on when those future ninjas will be released, soon™. 5 Kage Madara is basically a shark Kisame that can disperse buffs and shields when he uses his mystery. He definitely is better than Hokage Minato but he also works with fewer teams/lineups because a lot of teams require buffs to work (pretty much count all Earth and Wind teams out of ever using him).

Overall, both are very powerful and versatile ninjas. It comes down to your playstyle and what you want. I wanted Hokage Minato and I got him through a lucky stars event about a week after I got Jonin Minato. I used a Shisui, Windmain, Hokage Minato, and Kurenai team for nearly 5 months and I could beat people who had more pos1 int and 20k power because I could use Minato's mystery 3 rounds in a row and shisui twice with Dance wind main. If I was in your position, I'd go for the Hokage Minato fragments. He's appeared in quite a few events and we don't know when future ninjas are coming and they will probably be in events that the only reason to whale into is to get the ninja (not like Mission Mobi where you get a lot of other items from the gift boxes while getting the points for Hokage Minato).