Do the three creature cards need to be above Nether Shadow when the ability triggers, or when it resolves, or both?
Both. The triggered ability on Nether Shadow has what's called an intervening 'if' clause (glossary entry below). When the trigger condition occurs, beginning of upkeep, if the 'if' condition is not true, the ability doesn't trigger at all. If when the triggered ability resolves, the 'if' condition is not true, then the ability does nothing.
Intervening "If" Clause: Triggered abilities with a condition directly following the trigger event (for example, "When/Whenever/At [trigger], if [condition], [effect]") check for the condition to be true as part of the trigger event; if it isn't, the ability doesn't trigger. The ability checks the condition again on resolution. If it's not satisfied, the ability does nothing. Note that this mirrors the check for legal targets. Note that this rule doesn't apply to any triggered ability with an "if" condition elsewhere within its text. See rule 404.3.