Neuer, who has been out of action since suffering a second metatarsal fracture in six months in the 4-0 win over Mainz on 16 September 2017, resumed first-team training on Friday.
"We're all hugely delighted with how it's gone," Heynckes told media, after Neuer took part in the warm-up, as well as some ball drills.
"We've done everything right so far and the way he's worked is fantastic, but it's far too early to talk about [whether he'll play in the DFB Cup final or the UEFA Champions League final]. I know what I'm doing. I have a clear plan."
Watch: Manuel Neuer's top 5 Bundesliga saves
With the Bundesliga sewn up and only four league fixtures of the 2017/18 campaign remaining, Bayern's primary focus is on beating holders Real Madrid over two legs in their upcoming Champions League semi-final tie.
Should the five-time European champions succeed, they will advance to the final in Kiev, which takes place a week after the DFB Cup final against Eintracht Frankfurt, on 26 May.
It goes without saying that Neuer's return would be a real boon for club and country, especially with Germany's FIFA World Cup defence on the horizon.
At the same time, Heynckes has complete faith in second-choice keeper Sven Ulreich.
"His development has been phenomenal," the Bayern coach said of Ulreich, who has made 40 appearances in all competitions in Neuer's absence, conceding 34 goals.
"After Manuel Neuer, Ulreich is the second-best goalkeeper in the Bundesliga.
"He's fought his way through and has so much confidence right now that he won't be thinking about [what's going on with Neuer]."