Taking Malta is relatively straightforward; no rail gun required. You will however need 2-3 Tac bombers, 1-2 Medium bombers and an HQ to support them, plus your choice of Paratroopers (cheaper) or an Amphib corps (with the ability to attack it might save you a turn of bombing and get you a quicker capture). Don't bring any Maritime or Strat Bombers - they won't do much.
1) Use the Italian navy to reduce Malta fortress supply to 0 (only Battleships can do this so don't bother using Cruisers, they'll just take losses for nothing)
2) Place 1 naval unit (sub is often convenient) adjacent to both ports. You don't need to bomb the ports; just having 1 naval unit adjacent to the ports will prevent the land unit being able to gain supply from either port.
3) Spend 2, or if unlucky, 3, turns bombing Malta in the order of Medium bombers first, then Tacs. Repeat until AA unit destroyed. Thanks to your actions in step (2) above, it won't be able to reinforce.
4) Float your Paratroopers daintily into their new home. Or if you prefer, send your amphib.
If you want to be extra fancy, if you bring a Maritime Bomber, you can use this first to trigger both of the AA unit's 2 intercepts. Your Tacs and Medium bombers will then be free to unleash unmolested, reducing their losses significantly. The Maritime Bomber is very cheap to reinforce by comparison.
If you plan for a relatively swift capture of Malta (i.e. in 1940) then it's recommended to invest in Ground Attack ASAP as Tacs don't de-entrench without some tech upgrades, and this will slow things down considerably.
I could have sworn you had to have two naval units to blockade a port? Or is this different in WAW vs WIE?