For Giga Drain, its base power is 75. However:
If a Pokémon holding a Big Root uses a draining move or Strength Sap, it restores 30% more HP than it otherwise would. Additionally, a Pokémon holding a Big Root regains 30% more HP from Leech Seed, Ingrain and Aqua Ring.
If the user is holding a Big Root, the HP restored is increased by 30% (making the restored HP 65% of the damage dealt). Big Root does not increase the damage dealt.
For Magical Leaf, its base power is 60 and the Miracle Seed "Boosts the power of the holder's Grass-type moves by 20%"
This means that 60 x 1.2 = 72.
In conclusion, I'd recommend using Giga Drain due to its better power and open item slot.
(EDIT): In HGSS (AKA Gen IV), Giga Drain has base power of 60. So, in regards to Gen 4, I'd recommend using Magical Leaf w/Miracle Seed.