My 3 year old has had a cough only at night in bed for the last two nights, could this be whooping cough? i've had a sore throat for 2 days now too.

Not likely: If his vaccines are current. The cough is of short duration and appears to be contagious, likely a cold. Supportive care to include increased fluid intake, cool mist humidifier, saline drops/sprays, lemon& brown honey etc to relieve symptoms. If nocturnal persists / worsens after 1 to 2 weeks it will be necessary to consider other causes; nocturnal asthma, GE reflux etc.