Answer
There is more charge on the equivalent capacitance when the capacitors are in parallel.
Work Step by Step
Let $V$ be the battery voltage.
In series, the equivalent capacitance is $C_{eq} = \frac{C}{3}$
We can find the charge:
$q = C_{eq}~V = \frac{CV}{3}$
In parallel, the equivalent capacitance is $C_{eq} = 3C$
We can find the charge:
$q = C_{eq}~V = 3CV$
We can see that there is more charge on the equivalent capacitance when the capacitors are in parallel.
