The 26-year-old Crabtree had career highs last season with 85 receptions for 1,105 yards and nine touchdowns for the NFC champion Niners, and was a big reason they returned to the Super Bowl for the first time in 18 years. He sustained the injury during 7-on-7 drills in an organized team activity May 21.
"It's been very good. It's more November, middle to late November is kind of what we're hoping for," Harbaugh said. "He seems to be on track for that. That's what we're hopeful for, being able to play."
Crabtree recently resumed running as a significant step in his progress. His return will be a huge boost for a receiving corps searching for a complement opposite Anquan Boldin.
Even Harbaugh has been impressed with Crabtree's healing ability with an injury that often can take far longer than six months for full recovery.
"I catch it now and then, sometimes even when we're practicing he's doing his rehab work, pretty much talk to him every day and things seem to be going well," Harbaugh said. "He's been very positive and very upbeat and feels like things are progressing well."
Harbaugh has traded a few text messages with linebacker Aldon Smith, absent for the past two games while undergoing treatment for substance abuse, and the coach said there are encouraging signs Smith is getting himself right.
Smith, selected seventh overall in the 2011 draft out of Missouri, spent his 24th birthday in an in-patient facility Sept. 25. He is on an indefinite leave of absence.
There is no timetable for Smith's return, which could be as soon as after the bye week in early November. He also could face a suspension — either this season or early next year depending on how the league views his rehab stint — from the NFL following his arrest on suspicion of DUI on Sept 20.
"Heard that things are going very well, very positive reports back," Harbaugh said.
Smith's 19 ½ sacks last season were a franchise record.
Wideout Mario Manningham will be able to resume practice next week after spending the first six games on the physically unable to perform list, then the 49ers have three weeks to decide whether to add him to the 53-man roster.
Manningham made 42 receptions for 449 yards and one touchdown in 12 games and 10 starts last season before injuring his left knee in a loss at Seattle Dec. 23. He underwent reconstructive surgery to repair torn anterior cruciate and posterior cruciate ligaments.