Chibimoon's relationship with Pluto in the manga seems even deeper than her relationship with the Time Guardian in the anime, namely because we get to see more of it, and the fact that it is Pluto's death that serves as the catalyst to return Chibiusa to her normal self and trigger her henshin into Sailor Chibimoon which has been stalled for years.
All during the Crystal Tokyo storyline Chibiusa consistently identifies Pluto as "my only friend" and it's clear that the Guardian of Time feels a very strong maternal affinity for her as well. After all, she lets Chibiusa consistently hop through the time stream while she's ready to kill Sailor Moon for the taboo when she approaches. And there is of course the little bit where Sailor Pluto gives up her own life and commits the greatest taboo and stops time in an attempt to save her little friend Chibiusa.
It's understandable that they're so attached to each other. Being the Guardian of Time, Pluto is denied a life and children of her own. She's even denied the companionship of others. It is Chibiusa who finally breaks the rules and provides Pluto with companionship. She can find no solace among the people who surround her, and Pluto is afforded no people to find solace with. Together, they comfort each other. There is strong evidence that Chibiusa feels closer to Sailor Pluto than she does to her own mother, at least in the Crystal Tokyo story.
During the Death Buster Story, Pluto doesn't seem to have much time for her anymore. Her new duty is all encompassing and Chibiusa must find a new sailor senshi confidant and protector.