Well, its not really a fair comparison. First there is 6 F1 cars in GT3 in a variety of colors, and GT4 has only 1 F1 car in a variety of colours.
The best car in my opinion is the F090/S in GT3, as seen below (Black F1):
That being said, I found the F1 car was worse in GT4. In GT3, the variety of cars meant you could use certain versions for different races. Like the F 687 for the high speed tracks etc.
I felt too that the GT3's formula cars were better than the GT4's FGT.
But IMO the best was the F094 (or Polyphony 001 in PAL version), not the F090. F686 had most power though.