I unfortunately have doubts the story is true (but I can't say it is entirely debunked either).

None of the newspaper stories at the time mention ashes being dropped by airplane. The New York Times, with the most extensive coverage, just talks about a funeral at a Abyssianian Baptist Church (Fats Waller grew up with religion and first learned to play the organ), ending with the line.

Cremation took place at Maspeth, Queens.

This, incidentally, is notable in itself: African-Americans did not tend to get cremated at this time.

There was some sincere arguments by cremation advocates of the 19th century as an equalizer, as both "rich and poor" would result in the same final product, and that it would be more economical to (for example) ship remains overseas.

It is immoral, so to spend money which might buy bread for the people.

However, in practice, cremation was advocated to the elites, and there was contempt towards African Americans. The question was raised at the 1943 CAA convention who would allow "colored people" to be cremated at their location and only 12 raised their hands; the actual president of the CAA said the rules at his crematory only allowed Caucasians.

This was combined with the religious aspect: many African Americans were traditional Christians (note the Baptist church) and believed in the physical body being part of resurrection.

However, Fats Waller was a rich celebrity, and counted amongst other such notables as Albert Einstein and Humphrey Bogart who got cremated.

Here's the specific quote from the biography you mentioned:

The urn of ashes was turned over to an aviator known as the Black Ace, a pilot famous for his World War I and Spanish Civil War exploits.

The story exactly as printed is essentially impossible. There was nobody that matches this description. The closest that might fit is Eugene Jacques Bullard, who went to France from America to escape racism, who flew for the French in WW1 and in WW2, and did run a jazz club ("Le Grand Duc") between the wars which did get played at by none other than Fats Waller.

Bullard was also in New York at the time; he had gotten injured and went to the US in 1940, and picked up some odd jobs include being a language interpreter for Louis Armstrong. So he would have been the right place at the right time.

Note that still means the Spanish Civil War part is false, but this is possible misremembering or confusion; however, it certainly still counts as a ding against the story.

If the ashes were dropped by airplane, then it was done in a private manner, so there would haven't been any kind of "reaction". So the way people remembered him is attending the the service at the Church: 4,200 people attended. The church was overfull so people stood in the street outside and heard the service from a loudspeaker.

Gene Buck, former president of the American Society of Composers, Authors and Publishers, also eulogized Mr. Waller, saying "he brought great distinction to his family, his race, nation, colleagues and friends."

...

Prothero, S. (2002). Purified by Fire: A History of Cremation in America. University of California Press.