Since you would need the 'silverplate' version of a B-29 for delivery and evasion of the resulting blast, I'd think the way it would be delivered was the bombing plane would follow a mission profile for aerial reconnaissance. Weather and photo reconnaissance planes were common occurrences, and given fuel shortages by mid to late 1944, the Luftwaffe rarely bothered to intercept them.
The other profile would be for the delivery plane, flying at much higher altitude than a B-17 / 24 strike would follow one most of the way to a target before shifting off by itself to its own target. A single very high-flying plane, particularly in a heavy jamming environment, is likely to go unnoticed.
Since the plane would be flying at 30,000 feet + and 300+ knots it is all but immune to all but the heaviest flak guns, and those could likely be avoided. Most available Luftwaffe aircraft would have difficulty with an intercept at that altitude.
If the strike were coordinated with a fighter sweep in conjunction with other, conventional, raids it is likely the lone bomber would be ignored. The Germans, at least for the first and possibly next few, strikes wouldn't fully recognize the danger a single bomber posed to a city.