I will now list the strongest Maker per game.
Original: Nisa. The Heroine of Gamindustri stands above the rest as she was able to beat a monster that IF and Compa togther couldn't even hurt. With Gust, Red, and 5pb being more around IF and Compa's level, this is a clear victory for Nisa.
Second place could go to either IF thanks to her experience as a guild member or RED who IF calls quick.
Mk2:
1) Cave. She one-shotted a monster that base Nepgear couldn't affect (And IF stated that base Nepgear was stronger than herself). Her speed/Maneverability was also too much for Nepgear when Cave dragged her through a crowd. Lastly, she easily beat Nepgear in their splash fight.
2) Falcom. She was superior to Nepgear in their sparing match where Nepgear went all out (in base). Though she was pushed to use her full power, said full power quickly beat Nepgear with no issue (she did underestimate Nepgear in that Nepgear was a bit faster than she expected, so what was meant to be a fient attack ended up cutting Nepgear's shirt. This still puts Falcom well above base Nepgear). She is even better in Re;Birth 2 as she doesn't use her full power and is able to follow Nepgear the whole time with ease (still had the underestimating thing).
Victory/Re;Birth/Re;Birth 2/Re;Birth 3:
1) Tekken. The joke of her character (other than the masocist part) is her insane strength. Easily above the base form CPUs (accidentally gave Nep a 10 hit combo when she snuck up on her). The film pitch Vert gives Tekken has Tekken being superior to two HDD CPUs. Tekken doesn't question their strength, but it could just be Vert wanting to make Tekken look good as she wanted a fighting game surge in Leanbox.
It was questionable that she was that level of strength until Re;Birth 1 confirmed it. In Re;Birth 1 she directly blocks attacks by Fake Green Heart (a direct Copy of Green Heart). Being HDD level (at least) puts her above the other makers.
2) CyberConnect2. Here because of her rage mode. It was enough to impress Noire and fought along side her in HDD. It is strong, but we don't know how strong. Fighting alongside HDD could imply it being similar in power… but regular makers do that normally and don't scale to HDD so its hard to say.
U Action Unleashed:
Famistu/Dangekiko. With them being the only Playable makers in the game, they get this by default (IF was stated to have fought the CPUs and completed a larger Neptral Tower, but a little vague). Each has an item (end up getting 4.5 each) that is directly stated to be HDD level.
VS Zombies:
Tamsoft…I guess. Yeah, not a lot to go off of here. Fatmitsu and Dangekiko don't have their HDD item, so all three makers end up being around the same level and no one really does anything to stand above the rest. I get the feeling that Tamsoft is more of a fighter than the other two, but that is just my own opinion.
Megadimension:
0) Adult Neptune. Not a maker, but thought I'd mention her anyway. She is stronger than the other makers in the game and was able to match Vert and Nepgear (who both should have been in HDD given the circumstances) while not even going all out.
1) Million Aruther. Skilled fighter and her Knight summons gives her the edge over the other makers. She even has a deck of knights for serious battles.
2) Nitroplus. Her serious atitude would likely give her the edge over God Eater.
Vs. Segahard Girls:
IF since she is the only maker, duh. If you just go by side characters, than Uzume and Dreamcast are the strongest of the CPUs and Segahard girls (not counting God Segami).
Hyperdevotion Noire:
Lady Wac is likely the strongest General. She is stated to be one of the world's strongest generals, but no other general is given that type of fanfare. She is also stated to be able to one-shot all 4 CPUs if they were to make a mistake during battle. A quick reminder that 3 CPUs were able to beat all of the Generals (which yes does include Lady Wac) and yet the CPUs still realized how costly a mistake in a fight against Lady Wac would be.
4 Goddesses Online:
No playable sides. While not makers, Kiria and Princess are the other strongest players and were even stronger than the main group at different points in the game (without even accounting for the Cheat Tools).
Super Neptunia RPG
Chrome. Again, not a maker and this is really cheating since she is a former goddess…but she doesn't have a goddess form and is the only other playable character outside the four CPU so I'm including her. While she doesn't get her HDD form, she manages to retain that power.