That's a tough one. My four favorites couldn't be more different from one another even if they tried. So I'mma just give my four favorites.
1. Girls Last Tour
2. Gakkou Gurashi
3. Yagate Kimi ni Naru
4. Nichijou
Girls Last Tour: I watched the anime and absolutely adored it. Though short on main cast, Chii and Yuu are two of the most lovable protagonists I've ever seen in a story. The atmosphere was amazing, the sound design was wonderful. So I immediately went to read the manga after finishing episode 12. Tsukumizu's art is so simple but so unique. Of course, Chii and Yuu are still awesome and the atmosphere is just as beautiful and mysterious as it is in the anime. The ending crushed my soul.
Gakkou Gurashi: I picked this one up on a whim. The anime was good, but it wasn't anything jaw-dropping. But damn do I love the manga. First of all, not only does the anime change a lot of the major story in the manga, it completely changes the mood as well. The art in the manga is amazing. Particularly when shit starts to get serious. The artist knows their way around shadows and framing. The stakes are so much higher, the characters are so much more interesting (even before they leave the school, where the anime ends.) It's much much more effective as a psychological thriller. And with the end of the story seemingly approaching, I find myself really scared for the fates of my precious babies. (It's not looking good.)
Yagate Kimi ni Naru: I was really excited to hear this was getting an anime. A lot of people were worried it might turn out like Citrus and... Well I didn't think Citrus was *that* bad, but yes, the manga is way way way better. That said, the anime for Bloom into You is treating its source material right and that makes me really happy. Yagate Kimi ni Naru is my favorite romance series. My favorite things about the series admittedly don't have much to do with the romance itself. I like how it explores shit like impostor syndrome and figuring out your sexuality. But yes, Yuu and Touko's relationship is really cute.
And I'm glad Yuu has finally gotten her shit together and admitted to Touko that she liked her too.
There's a lot of small stuff in this series I really like. Subtle characterization, the cute and gentle feeling art work, how genuinely likable the cast is. etc etc.
Nichijou: I can't say much other than it's really funny and I really like Keiichi's art style. Nichijou is hands down my favorite comedy anime, and I was more than happy to find the manga didn't disappoint. It'll forever pain me to know we won't be getting a season two of Nichijou. There was a lot of good stuff in the manga which hadn't been used in the anime. Including but not limited to a really awesome flash forward to all the characters living their lives as adults.
I haven't read very many manga (yet) but I'd say my favorite one so far that I am presently caught up on is Bloom Into You. Yotsuba to is also a really fun read though.
Rurouni Kenshin
One Piece
Fullmetal Alchemist
Houshin Engi
Dragon Quest Dai no Daibouken
Detective Conan
Kekkaishi
Tsubasa Resevoir Chronicles
InuYasha
Ushio To Tora
Not the best if you ask me, but they're definitely my favorites and what I consider the best that I've read.
I guess it's a tie between Konohana Kitan (a mixture of meaningful stories and comedy, with beautiful art) and KonoSuba (adventure comedy about a group of adventurers whose group chemistry is that they have none).
I know that KonoSuba is originally a light novel, but still.
Its difficult to narrow its down to one so I'll just pick four but tbh tomorrow I would've probably picked four other manga so this isn't a definitive list.
Hunter X Hunter, 20th Century Boys, Shin Angyo Onshi and Fire Punch.
The controversial pick here is Fire Punch. I wouldn't say Fire Punch is at the same level as the other three from a writing perspective. A lot of people dislike it and its easy to see why. The reason I rate it so highly though is because of how much heart the manga has. The writing may not be the best and at times its plain silly but you can see how much emotion went into the manga. The raw feelings it evokes are like nothing else.
Don't want to spoil anything but I cried at the movie scene. It was done so beautifully that I felt I could feel what the characters where feeling. The silly childish parts where a welcome escape from how painful and depressing the manga was. Not many manga or any work of fiction are capable of invoking that emotional response from me. And for that I gotta give Fire Punch the credit it deserves.