When the tide is flooding, the current stronger going east towards the Delta. An ebb tide is when the water is going west towards the Golden Gate and the current is stronger going west. If the current is strongly going towards the gate and the winds are blowing towards the east, the conditions will be much more difficult. If you time your crossing when the current is not be influenced by tide in or tide out, you will only have the winds to deal with.
One note: in the spring, the current going west is always strong due to rain and snow melt runoff.