light dependent resistor circuits
A similar system is used for measuring chlorine concentration in water supplies, perhaps it could be adapted for your needs.
It uses two LDRs, one to measure the ambient light and one to measure light passing through liquid. It has the advantage that only the difference is used rather than an absolute level. Although small, the difference is easy to amplify to give better measurement resolution.
If that isn't a practical alternative, the LDR is still fairly easy to use in a potential divider. Connect it in a bridge configuration and measure it against a fixed value. That can be used to remove residual reading the you can amplify whats left to a larger voltage.
Incidentally, phototransistors operate MUCH faster than LDRs.
Brian.