I'm not currently in the classroom but I do lead professional development sessions on digital annotation tools along with ones that integrate with Canvas. My favorite tools are Hypothes.is, Perusall and Kami. In selecting what tool to use I've found it's not a matter of which one is the best. It's really a matter of what one lends itself towards your goals for what you want your students to do.
Kami is a great tool for individual annotations on a PDF and does have the ability to be shared and collaboratively annotated. This is more of a mark up on top of paper experience and the students can submit a share URL to a Canvas assignment to turn in their annotations.
Perusall is the cats meow of social PDF annotations and if that interests you, checkout @dhulsey Canvas and Perusall post and Canvas live demo.
Hypothes.is is the only tool I've mentioned that does HTML web page annotations as well as PDF annotations. They also are working on a Canvas LTI integration that allows students to turn in their annotations as an assignment and they are viewable in the SpeedGrader. Their education page has a lot of great resources for annotation strategies as well.
PS -- Since this is such a great question, I'm hoping we can find people in the Community that have ideas to share around this topic. I am going to unmark this as a question so that it can continue as a discussion (A question implies there is a correct answer). I'm also going to share this in the Higher Education community to see if there are some people there who are willing to share their annotation strategies.