Ellen Aguiar said she knew her son was distraught when he got on the boat, but she did not know what happened to him after he went to sea.
"The whole thing that surrounds this disappearance I find very suspicious and I just pray for the best," she said.
Richard Baron, Ellen Aguiar's attorney, has maintained that it was clear that Guma Aguiar did not want his wife to have control of his assets.
"The fact that the Absentee revoked Jamie's designation as his pre-need guardian and substituted his mother in May of this year (2012) further supports the conclusion that the Absentee does not want Jamie Aguiar handling his assets," Baron wrote in a legal filing on behalf of Ellen Aguiar.
A handwritten note on a 2011 legal filing obtained by ABCNews.com showed that Guma Aguiar objected to the appointment of his wife "to serve in any capacity" over his person or property.
"It's a family tragedy," Baron said. "As each day dwindles on, the hope of his being recovered is lessened. I think the reality may set in that Guma is not coming back."
When asked if she believed her son was still alive, Ellen Aguiar said, "I feel that he's at peace and I'm not giving up hope until I know for sure."
Ellen Aguiar has said that her son was emotional when he got on his boat because his wife had asked for a divorce, just hours before his disappearance.
Jamie Aguiar's attorney rejected the claim and said the couple wrote love notes, emails or texts to each other often and as recently as the day he disappeared.
Though the search for Aguiar has been called off, authorities say he is still considered a missing person and they are still investigating his disappearance. They are also trying to extract information from Aguiar's cell phone and the GPS on his boat, which Scherer said in court seems to indicate that Aguiar made several unusual turns on the boat before it drifted back to shore.
The devoutly Jewish Aguiar is known for being the main sponsor for an elite Israeli soccer team and making multi-million dollar charitable gifts to Jewish organizations. He has also had a number of personal transgressions.
He has been arrested several times, including for drug possession and driving under the influence, according to court records. He is also currently on probation after pleading no contest to domestic violence charges.
In 2010, he was involuntarily admitted to an Israeli psychiatric hospital after his erratic behavior.
Aguiar made his fortune in 2006 when he and his uncle Thomas Kaplan sold their Texas-based energy company for a reported $2.5 billion. The two have been in a messy legal battle since 2009 over the division of the money.
In 2011, he was appointed an emergency guardian after his wife and mother petitioned a Miami-Dade judge for one.
The couple has four children, the youngest of whom is 10 months old. They also have a 3-year-old son, a 4-year-old daughter and a 7-year-old son.