I stayed at the youth hostel international in Marseille and it was....ok. Clean and safe, but a lot of rules though. I was there during the offseason however, so most likely you will have more options that I did. I didn't spend much time in the city, but instead did some hiking along the coast. There are areas called "Les Calanque" that you HAVE TO VISIT. Well, if you like the outdoors anyway. Imagine little coves of clear blue water surrounded by white stone cliffs and mountains? Freakin beautiful. Pic here:
Les Calanque