。
The fee doesn't include the cost of the box.
Literal
Fee [in-には] box-cost [topic-は] is-not-included.
Two は-marked phrases serve different roles: には limits the scope ('within the fee'), while the second は marks 箱代 as the thing being commented on. The suffix 代 (だい) means 'cost of' — an extremely productive suffix for everyday expenses: 部屋代, 電気代, タクシー代.