Let's say that they each have their pros and cons...
Shonen Jump-
PROs: Since SJ has its magazine, as well as it's graphic novels, you can either buy individual manga titles or the magazine with multiple titles. So, that gives you more freedom in how you buy.
Also, the SJ graphic novels are two dollars cheaper (at least here they are). $8 a graphic novel! ^_^
Also, like someone else mentioned, it's like $30 for a year's subscription... that's about 300 pages in each mag, and 12 a year, that's 3600 pages of manga for $30!!
CONs: If you buy the magazine, you can't chose which manga are in there, and you may not like them, and not read them, and waste some money -_-"
This happens to me: You read the manga in the magazine, and still want to buy the novel to have in your possession, so you spend the money, but don't get to read anything new...
TokyoPop-
PROs: TokyoPop has a very wide variety of manga, which is great for people like me who like to experience new manga frequently ^_^
TokyoPop often keeps more of the original Japanese content, such as sound effects and Japanese references... which is nice to see the Japanese culture and you can learn a little too ^_^
CONs: It's at a higher price per novel than SJ... at $10 a volume... Hey, those extra $2 are important! LOL
All in all... I think both Shonen Jump and TokyoPop are awesome, especially for bringing us the world of manga :)