I consistently see this question asked a lot, so I wanted to save some folks the time by writing about my experience sifting through manga I purchased through Bookwalker JP. These titles are all roughly N5-N3 level and, most importantly, they include furigana.
I know furigana is a crutch, but allowing people to read some exciting content is a net positive.
This list is in order of difficulty:
Yotsuba&! (よつばと!)
A classic intro to manga that follows little Yotsuba and her adventures. It is a very good starter slice-of-life, but my only gripe is that because she is a child, she makes cutesy mistakes. It also lacks a lot of kanji, so beginners may not always know where to naturally pause between words. Which kanji definitely helps with.
Teasing Master Takagi-san (からかい上手の高木さん)
A very slow-burn romance manga following middle school kids and their seishun (youth). The language is simple and the kanji use is good. You'll find some great vocabulary centered around school drama and an early middle school setting.
Flying Witch (ふらいんぐうぃっち)
Honestly, I can't remember much except that it's a very slow slice-of-life. I eventually put it down because I didn't love it, but I remember the level being very manageable at around the N4/N3 range.
Shirokuma Cafe (しろくまカフェ)
One of my absolute favorites! Follow a lazy panda through his adventures with a motley cafe crew. It uses some tough words that rhyme or play into the polar bear's puns, but besides that, it is very manageable and I highly recommend it.
Horimiya (ホリミヤ)
I haven't finished this yet, but it's an intense high school romance that is quite exciting. The level definitely picks up here to a more natural pace. My only complaint is that the furigana feels super small and can be hard to read on Bookwalker.
SPY x FAMILY
This is a really popular anime/manga so I don't need to say much about it, but the level here is definitely on the edge of what I would consider manageable for an intermediate learner. There are a lot of fictional country names and spy terms, but nonetheless, it is still accessible via lookups thanks to the furigana on Bookwalker.
