Piper Jaffray’s Gene Munster, one of the few Apple (AAPL) analysts who attends product launches and counts heads, estimates that Apple sold 300,000 iPad 3Gs over the three-day launch weekend, including units pre-ordered online for Friday delivery. That’s the same number of units Apple sold in one day when the Wi-Fi-only model launched.

The lines at the stores Munster and his crew monitored — Apple’s Fifth Ave. store in New York City and a mall store outside Minneapolis — were shorter than those for the initial iPad launch on April 3 (329 vs. 730 and 119 vs. 132, respectively).

But given that customers had two and a half days to buy iPad 3Gs (versus one for the Wi-Fi model) and twice as long to put in pre-orders, Munster figures 300,000 sounds about right.

Adding those 300,000 units to the 500,000 iPads Apple sold the first week, plus the unknown number purchased in the intervening three weeks, Munster comes up with a total of more than a million iPads sold so far.

In a note to clients issued Sunday, Munster described his current sales estimate of 1.3 million iPads by the end of June — nearly two months from now — as “conservative.”

That’s an understatement, especially given that Apple is scheduled to begin selling the iPad overseas before the end of May.

But Munster may be forgiven for erring on the side of caution. In early April he published a first-day sales estimate of 600,000 to 700,000 only hours before Apple announced that it had sold only 300,000 iPads that day.

Munster’s team called 50 Apple Stores on Sunday and found that 49 of them had sold out of iPad 3Gs and most had run out of Wi-Fi-only models as well. But it’s not clear whether that’s because demand was high or supplies were low. Munster believes it was probably a bit of both.

“Near-term,” he writes, “this may put downward pressure on launch day/weekend statistics, but long-term we see it as a positive, as consumers are definitely interested in the iPad as a new category.”

See also:

• iPad 3G draws hundreds in New York
• New iPad launch-day estimate: 600,000-700,000 sold
• Predicting iPad sales: How close were the analysts?
• How many iPads will Apple sell?

[Follow Philip Elmer-DeWitt on Twitter @philiped]