You're thinking of the Age of Unreason series by J. Gregory Keyes.
The first book is Newton's Cannon:
A dazzling quest whose outcome will raise humanity to unparalleled heights of glory--or ring down a curtain of endless night . . .
1681: When Sir Isaac Newton turns his restless mind to the ancient art of alchemy, he unleashes Philosopher's Mercury, a primal source of matter and a key to manipulating the four elements of Earth, Air, Fire, and Water. Now, as France and England battle for its control, Louis XIV calls for a new weapon--a mysterious device known only as Newton's Cannon.
Half a world away, a young apprentice named Benjamin Franklin stumbles across a dangerous secret. Pursued by a deadly enemy--half scientist, half sorcerer--Ben makes his fugitive way to England. Only Newton himself can help him now. But who will help Sir Isaac? For he was not the first to unleash the Philosopher's Mercury. Others were there before him. Creatures as scornful of science as they are of mankind. And burning to be rid of both . . .
The "Jesus Shoes" show up in the second book, A Calculus of Angels.
Robert lifted his wooden tankard. "To your new invention, the Jesus shoes!" he pronounced.
"Hush, you butterhead!" Ben said, nearly choking on his drink. "Now who's being incautious around the Romish?"
Robert grinned and took a gulp of his beer. "An eagle abroad but an owl at home," he quoted.
"So what do you call those things?" He gestured vaguely beneath the table.
"Aquapeds," Ben replied.
"Of course. Nothing is scientifical unless you name it in the Latin," Robert remarked, a bit mockingly.
The bit with the meteor looks to have happened at the end of the book. It's referenced once in the second book:
Ben fidgeted. He and Newton had not explained what had really happened two years before: that the meteor had been intentionally summoned, not by God, but by men.
The prince laughed at Ben's expression, perhaps mistaking it for an intense effort to address is argument. "Who can know how God works? Certainly not I. I am no theologian."
"Do you wish for Sir Isaac and me to cease our experiments?"
And Goodreads mentions it in the summary:
1722: A second Dark Age looms. An asteroid has devastated the Earth, called down by dire creatures who plot against the world of men. The brilliant-- some say mad--Isaac Newton has taken refuge in ancient Prague. There, with his young apprentice Ben Franklin, he plumbs the secrets of the aetheric beings who have so nearly destroyed humanity.
I found the book searching with a string of science fiction book alchemy "jesus shoes" -"sweet tea" (There's a book named Jesus Shoes and Sweet Tea that kept confounding my results) and near the bottom was an EText at a Russian pirate site which provided the correct quote.