The story is "The Homework Horror" by Greg Cox. It was originally printed in Amazing Stories Vol. 62 #1, but was reprinted in Bruce Coville's Book of Nightmares II: More Tales to Make You Scream, which is probably where you read it.
And the evil number in the book is 5, not 3.
Five stayed in the shadows and kept her distance. Until 5:55.
At that moment, as soon as the numbers on the digital clock changed over, five slided down the wall and onto the floor. Before Danny could move, five's curved tail hooked around his feet and pulled shut. Barbed-wire teeth stabbed him through his socks. Danny's body jerked. He dropped the report card. The radiator suddenly clicked on and newborn air currents blew the card, complete with its shiny little sticker, all the way across the room.
Five tightened her grip, grinding Danny's ankles together painfully. Even as he cried out, though, he refused to surrender. He could still see his golden star. Five was not in charge here, Danny knew, not as long as he could still remember how to add.
With his small right hand, Danny grabbed the giant five by her single ver-tical bar, then stood up, partially dragging the hissing number from the plane of the floor. He reached for the clock-radio with his other hand. It was still slightly too far away. Without letting go of five, Danny stretched his arm until a few fingers just grazed the clock's plastic face. He held his breath and tried to visualize a plus sign between the five and the clock.
For a second, he really saw it: two crossed bars of intangible light hanging before his eyes. Then a momentary flash of green to the left of his head attracted him. Danny turned and saw the numbers of the digital clock jump instantly from 5:55 to 6:00 P.M.
Five's jagged tail loosened and pulled away, and Danny kicked his feet apart. He felt five's thin neck shrink between his fingers. Downstairs, the cuckoo clock released the first of a half-dozen enthusiastic chirps.
Danny gave his clock a friendly pat. "Way to go, little six. You did good!"
The glowing green number flickered once, as if to agree.
UPDATE: I did an embarrassing amount of research to confirm this.
First, I went to Google and just searched for "short story evil number" and got this LibraryThing post which seemed similar and offered a little more detail about the boy doing homework and the number possibly being 5. Since it was more detailed, I went to Google Books and searched for books between 1980 and 2000 that had the words homework and 5:55 in it and proceeded to just walk through all the results (Google Books search would be a lot better if you could just filter between non-fiction and fiction!)
And then there, on page 9 of the results, was the Amazing Stories result which unfortunately you only get snippet view, so I searched for the phrases around the phrase I found to get some different snippets to do some more research, and it clearly was the story the LibraryThing poster had read, and since it involves the number 5 being able to come out of a clock at 5:55, to me it's the story zompz read.
Unfortunately, because it was just a snippet view, it didn't have the author or the story, and the Google Books link has an extremely blurry and basically worthless table of contents. But it said Amazing Stories Volume 61, 1987, so I went searching.
Turns out Amazing Stories volumes are printed bimonthly, so there were 6 issues of Volume 61 - and they also overlap years, so Volume 62 also kicked off in 1987. I knew the story was on page 122 (from the Google Books result), and some Locus searching led me to conclude the story was called "The Homework Horror", which is actually from Volume 62, issue 1, not Volume 61 (the Google Book that was scanned is probably an anthology.)
And then it was easy to see that the story had been reprinted in the Bruce Coville anthology, which are exactly the same kinds of books I was reading in the early 90s so QED.
UPDATE: I emailed Greg Cox about the question, here's his response:
Wow. I had no idea people were still talking about that story, which I haven't thought of for years. I can't speak for the original questioner of course, but that description sure sounds like my story, which I wrote nearly thirty years ago!