I don't know if they're the best, but they are some ot the best. Definitely.

I think it's absolutely a good thing to branch out and try different types of comics. While the independent comics have more freedom for new ideas many times they also lack a history and an epicness that you might find with the major publishers.  
 
What I don't like is when you get the elitists who believe they are somehow better or more enlightened because they read those books. 

I feel the need to get into more obscurer comics for satisfying stories though I seldom do.

Mainstream comics have to follow a bureaucratic structure. Indie titles have significantly higher potential.

i also have to agree. with indie comics they are more than able to take more risks because so more often then not they will not be able to last long and have a very finite number of issues available. when you have a ticking clock all your creativity can spill out without fear of your comic being rejected and when that type of unrestrained passion is put in a comic most readers can feel it and the comic transcends from being just another comic into something much more. the saddest part is the money and perks that come from being published in a big comic company like DC, Marvel, etc. also comes with restraints that stem the real creativity from its authors and in all honesty the only people involved who really are allowed to shine are the artists. 

At risk of sounding like a hipster, I have to agree with you, and I feel that there's a few reasons that this is true. The less mainstream titles tend to have smaller production teams, which in turn leads to more direct creative control and communication between all parties involved. Many of these titles are also targeting a specific demographic of reader, whereas many big names are trying to appeal to as broad an audience as possible. This means that the little guys can focus more on what they want to do with the stories and characters, rather than trying to contort everything for marketing reasons.