It would help if the comment system was rejiggered so that it's much easier to discourage negativity.
Direct replies chains so negative commentors can be ignored/pushed out of the discussion.
Upvotes/downvotes for the same reason
Report buttons and a ban system.
A reputation system, that give a % chance of hiding a users comment, or starts them with downvotes, or adds a delay timer to comment visibility.
A friend/acquaintance system so that you can have a soft bans that makes a user only visible to the people who have friended them/direct replied to them.
Comment order randomisation, because first comments are more emotional so it's not good to put them at the top of the discussion.
Instead of "BBCode allowed" as the default reply text change it to "The scanslators have worked hard to bring you this chapter, say something nice back" to encourage reciprocity.
Put a positivity meter at the top of each comment section that will lock the thread if there isn't enough, to remind people that the comment sections are a scarcity and that they should use it to its best while they still can.
Give positive commenters awards that show how knowlegable or veteran or proactive they are so they get more attention than negative commenters, to make them more authorative and encourage others to follow their lead.
Have commenters answer a question before commenting like "pick one: This manga is; cute☐ cool☐ interesting☐ beautiful☐ etc.☐", to encourage consistency in positivity.
Have a bot that puts the comment from the Scanlators as the first comment, even if it's just a generic compliment like "Thank you for all the help and positive comments, it's fun to hear from people who love manga as much as we do" by default that can be edited by the scanslator to personalise it. It's harder for people to be dicks if you can get them to like the scanslator.
Add a tag next to their username saying "one of the 99.3% of users that left a positive comment on this series" to let people know that the negative users are just a small vocal minority.
Lots of stuff you can do to foster a more positive mangadex community.