The most complete story of the three Legendary Beasts (Raikou, Entei, and Suicune) was told in Pokémon Generations episode 6 "The Reawakening". From Bulbapedia's summary:
Eusine looks around and begins recalling how the Brass Tower burned down long ago. It was once a beautiful place deeply admired by the townspeople of Ecruteak City, until it was struck by lightning and was engulfed in flames. Three nameless Pokémon perished in the fire, much to the despair of the townspeople. After the fire went out, a rainbow came down from the sky and Ho-Oh appeared. Ho-Oh used its mystical powers to revive the perished Pokémon into Raikou, Entei and Suicune. The three Legendary beasts appeared on top of the remnants of Brass Tower, leaving the townspeople of Ecruteak City in awe.
The "nameless Pokémon" that became the Legendary Beasts appear like this:
Who's that Pokémon?
It's…nobody we know!
These silhouettes don't match that of any Eevee evolutions or any other Pokémon we've seen so far (to me, they look much closer to a real-world wolf).
Since Pokémon Generations is intended to be much closer to the games than the main anime staring Ash, I think it is closer to being a "definitive" version of the story. Thus it's safe to say that these three are indeed unknown Pokémon and that the theory that they were Eeveelutions is debunked.