Naruto is a good series, yes. But best? Far from it in my opinion.
The anime/manga world has so much to offer. My personal all-time favorite is a manga named 20th Century Boys. It has one of the best mystery stories I have ever seen and combines it with fantastic character development. It takes the somewhat overused idea of kids growing up to save the world and turns it into a dark, complex plot in which the cast must discover the hidden secrets of their pasts to prevent tragedy from destroying the world and it's portrayed brilliantly. I personally cannot see how Naruto can compare.
Animewise there is Gurren Lagann. Gurren Lagann looks like it would be a cliched action mecha but it really isn't. Sure, it starts off pretty simple and the plot isn't really THAT deep but that's why it's so good: it tricks you into thinking it's mindless action and then things escalate. Gurren Lagann is a story of tragedy, despair, betrayal, hope, and perseverance. It's the story of how oppression can force determined humans to rise up and grab hold of the futures they seek for themselves. It's the story of how those who wish for the good of the world (or the universe) may be driven to "evil" for the greater good, even if it looks like horrific chaos on the surface. It's the story of a weak boy who grows up and suffers tremendously yet still pursues a brighter future and it's because of this that it may be so simple yet so deep at the same time.
There are a number of other awesome ones as well (Fullmetal Alchemist, Code Geass, Clannad, Future Diary, Liar Game, Steins;Gate, Zatch Bell, etc.) that also capture their own amazing essence in a way few other stories can replicate. I don't have the time (or desire) to focus on every one of those but the point is that as good as Naruto is, I just can't say it is the best. The plot gets weak too many times and the side characters get shafted for too long for me to say that Naruto is a top tier series.